September 06, 2012

ASHG 2012 abstracts are online!

There is so much good stuff there. This year I decided against posting the full abstracts, so I'll just link to a few, adding a few sentences on why they strike me as interesting. And, since there are so many interesting ones, I'll keep updating this entry.

On the Sardinian ancestry of the Tyrolean Iceman confirms that modern Sardinians are most similar to both the Tyrolean Iceman and the Swedish Neolithic TRB individual (presumably Gok4). You can find my analysis of both in the archives of the blog. But, look here:

Strikingly, an analysis including novel ancient DNA data from an early Iron Age individual from Bulgaria also shows the strongest affinity of this individual with modern-day Sardinians. Our results show that the Tyrolean Iceman was not a recent migrant from Sardinia, but rather that among contemporary Europeans, Sardinians represent the population most closely related to populations present in the Southern Alpine region around 5000 years ago. The genetic affinity of ancient DNA samples from distant parts of Europe with Sardinians also suggests that this genetic signature was much more widespread across Europe during the Bronze Age.

As you may have guessed, I can't wait to get my hands on that Iron Age Thracian. His similarity with Sardinians is striking, because by the Iron Age, I would have thought that something akin to the modern genetic landscape would have begun to crystallize in Europe.

Y Chromosome J Haplogroups trace post glacial period expansion from Turkey and Caucasus into the Middle East confirms what I have argued about, i.e., that the West Asian highlands are responsible for the spread of haplogroup J, including, it seems into the Middle East itself. The chronology presented probably assumes the evolutionary mutation rate; also, the lack of haplogroup J in Europe pre-5ka argues for a late expansion. I am fairly convinced that out of this West Asian highlander population came the two dominant groups of West Eurasian prehistory, the Indo-Europeans and the Semites, their spread associated with a "metallurgical edge" in technology and social complexity during the Late Neolithic and Bronze Age. The latter probably picked their language from a T- or E-bearing population of the southern Levant (Ghassulians?), as these two haplogroups might link the Proto-Semites with their African Afroasiatic brethren.

We estimate that Eurasian populations split from ancient Africans at 58,000-120,800 years ago, and the divergence time of Europeans and Asians occurred at 35,750-70,500 years ago.

This sounds reasonable, and the wide confidence intervals probably reflect current uncertainties about the mutation rate. The European/Asian split time intersects the UP and postdates the ~70ka turning point (Toba + Drying up of Arabia/Sahara). The African/European split time intersects the ~106ka Nubian complex in Arabia.

We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.

This might seem superficially at odds with the recent finding of greater Neandertal ancestry in East Asians than Europeans, but remember that levels of Neandertal admixture depend on allele frequencies of introgressed variants, and East Asians are generally less polymorphic than Europeans.

Totally, we identified 410,683 archaic segments in 909 non-African individuals with averaged segment length 83,460bp. In the genealogy of each archaic segment with Neanderthal, Denisovan, African and chimpanzee segments, 77~81% archaic segment coalesced first with Neanderthal, 4~8% coalesced first with Denisovan, and 14% coalesced first with neither, validating the algorithm. Interestingly, a large proportion of all the archaic segments identified shared 88.9% similarity with Neanderthal, suggesting a single major admixture with Neanderthal at 82~121kya, right after the Africa exodus of the ancestors of modern humans.

It will be interesting to see what these authors get a different date than Sankararaman et al. The mutation rate can't be at fault because these dates are mostly dependent on the recombination rate. My initial guess is that the lower rate of S. et al. may be due to limiting the analysis to alleles with MAF less than 0.1. As I said before, it is unclear whether admixture LD-based signals of admixture with Neandertals can account for the totality of the D-statistics of Non-Africans vs. Africans.

Sequencing of an extended pedigree in Western chimpanzees is interesting for a variety of reasons, but for me the primary one is the inevitable use of this pedigree to fix the chimpanzee autosomal mutation rate, which has so far been assumed to be similar to the human one. On a similar topic, Estimating human mutation rate using autozygosity in a founder population comes up with 1.21x10-8/bp/generation for humans, which is practically the same as that inferred for Iceland, and belongs to the class of slow mutation rates that have been inferred lately and which may reshape our understanding of events ranging from human-chimp speciation to the date of Out-of-Africa.

Comparison of the variation within autosomal and haploid data sets of studied Western Balkan populations revealed their genetic closeness regardless of a genetic system inspected, in particular among the Slavic speakers. Hence, culturally diverse Western Balkan populations are genetically very similar to each other. Only the Kosovars show slight differences both in the variance of autosomal and uniparentally inherited markers from the other populations of the region, possibly also due to their historically strict patrilineality. In a more general perspective, our results reveal clear genetic continuity between the Near Eastern and European populations, lending further credence to extensive, likely multiple and possibly bidirectional ancient gene flows between the Near East and Europe, cutting through the Balkans.

Asian Expansion of Modern Human out of Africa is not very eloquent, and I think may be missing a zero in one of its numbers, but the point being made (that the major Y-haplogroup E found in Africans is descended from Asian back-migrants) is something which I also think very likely, for reasons explained here.

Paleolithic human migrations in East Eurasia remains largely unknown due to the lack of sufficient markers derived from the mutations that occurred during that time frame. To tackle this problem, using the sequence capturing, barcoding technology and next-generation sequencing, we identified more than 4,000 new SNPs encompassing most single copy non-recombining region of human Y chromosome. New clades for haplogroups O, C, N, D, and Q could be geographically located. Especially, a few star-like expansions were unveiled, showing strong population growth. The phylogeny of Haplogroup N was radically rearranged, and all the N individuals could now be categorized into either a northern clade N1 or southern clade N2, revealing a Paleolithic migratory routes of the ancestors of Uralic speaking populations. Haplogroup C, especially the East Eurasia-dominant clade C3, could also be separated into at least two ancient clades, suggesting Paleolithic migrations in East Asia. Three major clades under O, M117+, M134xM117, and 002611+, each could be now further classified into several subclades. With these new findings, we proposed the modified the routes and dates for human populations’ migration, especially those in Paleolithic time. A few Y-chromosomal expansions could now be linked to certain prehistoric cultures or ancestors of language families.

Applying this methodology to data from self-identified AJ samples, we show 85-90% of them belong to a genetic isolate related to other Mid-Eastern populations. This group has experienced an extreme bottleneck 30-35 generations ago, with subsequent expansion greatly exceeding the growth rate across all humans. Data are consistent with bottleneck size of merely 400 founders.

13 comments:

Suggesting that J's southernmost branches adopted their Afroasiatic language after encountering (or becoming?) Ghassulians make little to no sense since this culture inscribes itself within a timeframe which does not fit within the glottochronology of Proto-Semitic (understand its earliest layers and not the break up).

The interaction you are referring to (between african afroasiatic speakers and PPNB agro-pastoralists) fits within the spectrum of Juris Zarins Circum Arabian Nomadic Pastoral Complex which supposedly spread Semitic throughout the area.

It is also simplistic to assume that these PPNB populations simply shifted their language, as PS is hypothesized to have had early ergative features (some of which can be observed in Aramaic)... Typologically, this is proves to be an interesting link to Northeast Caucasian languages which also exhibit extensive properties (and whose speakers have high J-M267 frequencies).

I am really looking forward to the new Y-DNA J paper! This is a very needed one I would say. So they seem to be arguing for a late expansion of haplogroup J out of the northern areas of the Near East and the Caucasus it seems? The lack of J in Neolithic European remains is interesting as well. Maybe J did not expand until very late indeed? I wonder which pre-historic culture J1 and J2 may be associated with?

Doesn't your point about Afro-Asiatic expanding from NE Africa/the Levant suggest against referring to northerly J-bearing populations as 'Semites', and rather, for describing the original E/T Ghassulian-or-whatever substratum as proto-Semitic?

Thanks Dienekes. I am particularly following your comments and updates regarding the 'invasion' of Europe some time after 5000 years ago. It's a test of one of my own theories: Whatever actually happened to provoke the 'Great Flood' and 'Table of Nations' Biblical accounts, the actual outcome in our world of the events behind those stores was this: 4 men with a new form of J flavoured Y-chromosomal DNA appeared in the area of Mount Ararat (in Anatolia) in the middle of the 4000s BC. Over time, those 4 men spread their form of J flavoured Y-DNA remarkably widely into the peoples around them, and as their genes spread, many nations were established - including a large number (all?) of the Indo-European and Semitic nations.

A bottleneck down to an effective population size of four hundred individuals ca. 1100 CE-1250 CE, would suggest that a lot of the genetic diversity reducting in Ashkenazim is due to pogroms (perhaps fueled by the same surge of religious sentiment that fueled the contemporaneous Crusades), rather than by Founder effects at the time of the Jewish diaspora ca. 70 CE, or perhaps alternately, at the time of the fall of the Roman empire, or by increasing intolerance of non-Christians during the late Roman era.

All of these events have been acknowledged historically as notable, but few people would have expected the bottleneck effects at the time of the late Middle Ages to be more intense than those at earlier times.

In essence, this study suggests that this era saw a "grass roots" Holocaust urged on by the Pope and leading European kings that was more catastrophic than the one that took place during the WWII Holocaust itself.

Doesn't your point about Afro-Asiatic expanding from NE Africa/the Levant suggest against referring to northerly J-bearing populations as 'Semites', and rather, for describing the original E/T Ghassulian-or-whatever substratum as proto-Semitic?

The E/T-whatever people were speaking some kind of Afroasiatic, and when they mixed with the J1 people some kind of "Proto-Semitic" was formed. This "Proto-Semitic" then split ~5ka:

And, subsequently it was the mixed J1/E/T/whatever population that spread Semitic languages around.

The J1 people who stayed behind in the north (and didn't mix with the E/T Afroasiatics) continued to speak their own languages (perhaps some type of Northeast Caucasian-type language or others that are now extinct).

Dienekes, don't you think the Bronze Age is too late to be associated with IE entering Europe? However, I could see the further spread and eventual split of Celtic/Italic/Germanic within Europe from some Danubian/Balkan core region dating to the Bronze age. Also, within Europe, J is mostly high along the Mediterranean shores (and also North African shores), i.e., regions that mostly got IE rather late, if at all, and low in regions of former Celtic and Germanic languages that arguably spoke IE earlier (and lowest in Slavic speakers).

I am not surprised by the genetic affinity of Western Balkans, and the fact that Kosovars stand out, a little (see example:)

"don't you think the Bronze Age is too late to be associated with IE entering Europe?:

1. The Celtic/Italic/Germanic waves are a fit to Urnfield which moves into their urheimats ca. 1300 BCE in the late Bronze Age.

2. Indo-Aryans arrive in South Asia about 2000 BCE with room to be a up to few hundred years older if new digs find something a bit older.

3. Hittite expansion starts in the Bronze Age at about 2000 BCE and leads to the end of Hattic languages. There is not bona fide dispute over when IE became the only language family in Anatolia (perhaps aside from an outlier community or two in the far eastern mountains), even if there is dispute over the pre-Hittite language mix in Anatolia.

4. IE-Ancient Greek replaces the mainland pre-Greek language and Minoan in the early Bronze Age.

5. Slavic expansion comes much later, not earlier than 200 CE, and erases most linguistic clues about earlier language in the Slavic region.

6. Corded Ware was very likely IE and dates from ca. 3000 BCE (at the earliest Polish sites) to 2400 BCE at its greatest extent, generally moving E to W during the Copper age to Bronze age transition. If you average your genetic data across Europe, the transition date looks early Bronze Age.

8. My best guess is that Bell Beaker is a non-IE proto-Vasconic superstate imposed on a Neolithic megalithic culture substrate, with the two waves combined mostly replacing local Mesolithic people.

9. IMHO, the megalithic Funnelbeaker (TRB) people were a decline phase of the LBK wave under pressure from both Pit Ware and the emerging IE people which reaches a tipping point ca, 2900BCE-2400BCE when IE gains a decisive edge over TRB. TRB is probably where most admixture of Northern and Sardinian takes place.

10. IE is confined to a proto-IE Yamna culture limited to the Pontic steppe until the dawn of the Bronze Age (with perhaps a small proto-Tocharian group leaving ca. 3500 BCE and arrive in Tarim Basin ca. 2000 BCE, and a proto-Corded Ware group leaving for Poland ca. 3000 BCE).

I think there is something wrong with the Ashkenazi data, at least in terms of the number of generations.

There is nothing historical to limit the Ashkenazi to 400 founders at anything like the necessary date. The only way this can possibly be true is if the Ashkenazi descend soley from the Jews of the kingdom slavo/Baltic of Litva. While Western Jews suffered a lot of massacres, there was a great deal of migration to Poland joining an established safe community, and thence to Litva.

You are mostly saying something similar to my statement: IE did not enter Europe during the Bronze age, but was already present and then further spread and diversified just before and during the Bronze Age.

A couple of other comments:

8. My best guess is that Bell Beaker is a non-IE proto-Vasconic superstate imposed on a Neolithic megalithic culture substrate, with the two waves combined mostly replacing local Mesolithic people.

In most of Europe, Bell Beaker did not replace anything. Outside of Iberia, the density of Bell Beaker sites makes only up about 10% in most areas, and perhaps 25% to 30% in the densest ones, compared to all agricultural settlements. And the latter show local continuity but are contemporaneous with their Bell Beaker neighbors.

I think there is a good chance Bell Beaker was proto-Celtic (perhaps leaning a bit towards proto-Italic) - possibly related to Sorothaptic/Lusitanian.

6. Corded Ware was very likely IE and dates from ca. 3000 BCE (at the earliest Polish sites) to 2400 BCE at its greatest extent, generally moving E to W during the Copper age to Bronze age transition.

The problem is that west of the Vistula, Corded Ware is an unintrusive evolution from TRB and Globular Amphora. There is strong local archaeological continuity, with continued use of megalithic and GA grave sites. There are many sites with mixed TRB and GA ceramic, and a ~300 year overlap. Also, towards the west this region is (and was) much higher in haplogroups I and R1b than R1a. Finally, copper import into TRB and later Bronze Age influence is from the south - not east. Generally, the (far) eastern TRB is very different from the southern and northern groups (the latter includes parts of Poland, all of coastal Poland, and the Baltics), which show no archaeological Kurgan connection.

Alternatively, PIE could have had a pre-Bronze Age footing in Europe with the large-population Cucuteni-Trypillian, which could have made Yamna IE when these lived in parallel (and also when later climate change forced these agriculturalist to either become pastoralists, or move west).

Interestingly, the related Hamangia culture had links to Anatolia. I am convinced that there is a very early PIE connection across the Black Sea.

Other nearby cultures that could have been IE early on are Lengyel, Baden and very likely Globular Amphora. Of course, if one follows this train of thought, PIE in Europe and its Anatolian connection could go as far back as LBK...

I don't see IE people as steppe folks, at all - I believe they are the agriculturalists from former wetter areas of Romania and the Ukraine that needed to move W/NW due to climate change. Globular Amphora fits this well with their haphazard lifestyle (few houses found are small - so are settlements; emphasis on raising pig and cattle over growing grain) and its extent from Ukraine to Lower Saxony. Note again like later with Corded Ware, west of the Vistula evidence is that these people integrated with (at lowish density) rather than replaced TRB.

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